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  <section id="advanced-usage">
<h1>Advanced Usage<a class="headerlink" href="#advanced-usage" title="Link to this heading">¶</a></h1>
<section id="docker-container-installation-and-usage">
<h2>Docker Container Installation and Usage<a class="headerlink" href="#docker-container-installation-and-usage" title="Link to this heading">¶</a></h2>
<p>A Dockerfile has also been provided to run TIMSCONVERT inside a Docker container.</p>
<ol class="arabic">
<li><p>Build the Docker image.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">build</span> <span class="o">--</span><span class="n">tag</span> <span class="n">timsconvert</span> <span class="o">-</span><span class="n">f</span> <span class="p">[</span><span class="n">path</span> <span class="n">to</span><span class="p">]</span><span class="o">/</span><span class="n">timsconvert</span><span class="o">/</span><span class="n">Dockerfile</span> <span class="o">.</span>
</pre></div>
</div>
</li>
<li><p>Run the Docker image in a container.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">docker</span> <span class="n">run</span> <span class="o">--</span><span class="n">rm</span> <span class="o">-</span><span class="n">it</span> <span class="o">-</span><span class="n">v</span> <span class="p">[</span><span class="n">path</span> <span class="n">to</span> <span class="n">data</span><span class="p">]:</span><span class="o">/</span><span class="n">data</span> <span class="n">timsconvert</span> <span class="o">--</span><span class="nb">input</span> <span class="o">/</span><span class="n">data</span> <span class="o">--</span><span class="n">outdir</span> <span class="o">/</span><span class="n">data</span>
</pre></div>
</div>
</li>
</ol>
</section>
<section id="nextflow-installation-and-usage">
<h2>Nextflow Installation and Usage<a class="headerlink" href="#nextflow-installation-and-usage" title="Link to this heading">¶</a></h2>
<p>A Nextflow workflow has also been provided to run TIMSCONVERT.</p>
<ol class="arabic">
<li><p>Create a conda instance. You must be using Python 3.11. Newer versions of Python are not guaranteed to be compatible with Bruker’s API in Linux.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">create</span> <span class="o">-</span><span class="n">n</span> <span class="n">timsconvert</span> <span class="n">python</span><span class="o">=</span><span class="mf">3.11</span>
</pre></div>
</div>
</li>
<li><p>Activate conda environment.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">activate</span> <span class="n">timsconvert</span>
</pre></div>
</div>
</li>
<li><p>Install <a class="reference external" href="https://www.nextflow.io/">Nextflow</a> to your <code class="docutils literal notranslate"><span class="pre">conda</span></code> environment.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">conda</span> <span class="n">install</span> <span class="o">-</span><span class="n">c</span> <span class="n">bioconda</span> <span class="n">nextflow</span>
</pre></div>
</div>
</li>
</ol>
<ol class="arabic" start="3">
<li><p>Download TIMSCONVERT by cloning the Github repo.</p>
<ul class="simple">
<li><p>You will need to have <a class="reference external" href="https://git-scm.com/downloads">Git</a> installed and ensure that the option to enable symbolic links was checked during installation.</p></li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">gtluu</span><span class="o">/</span><span class="n">timsconvert</span>
</pre></div>
</div>
<ul class="simple">
<li><p>It may be necessary to explicitly allow for the use of symbolic links by adding the -c core.symlinks=True</p></li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="o">-</span><span class="n">c</span> <span class="n">core</span><span class="o">.</span><span class="n">symlinks</span><span class="o">=</span><span class="n">true</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">gtluu</span><span class="o">/</span><span class="n">timsconvert</span>
</pre></div>
</div>
</li>
<li><p>Install TIMSCONVERT’s dependencies via <code class="docutils literal notranslate"><span class="pre">pip</span></code>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">-</span><span class="n">r</span> <span class="p">[</span><span class="n">path</span> <span class="n">to</span> <span class="n">timsconvert</span> <span class="n">directory</span><span class="p">]</span><span class="o">/</span><span class="n">requirements</span><span class="o">.</span><span class="n">txt</span>
</pre></div>
</div>
</li>
<li><p>You will also need to install our forked version of <code class="docutils literal notranslate"><span class="pre">pyimzML</span></code>, which has added support for ion mobility arrays in imzML data from imaging mass spectrometry experiments.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">gtluu</span><span class="o">/</span><span class="n">pyimzML</span>
</pre></div>
</div>
</li>
<li><p>Configure <code class="docutils literal notranslate"><span class="pre">nextflow.nf</span></code> script to your liking. See <a class="reference internal" href="local.html"><span class="doc">Local Usage</span></a> for a list of parameters.</p></li>
<li><p>Run TIMSCONVERT in Nextflow.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">nextflow</span> <span class="n">run</span> <span class="p">[</span><span class="n">path</span> <span class="n">to</span> <span class="n">timsconvert</span><span class="p">]</span><span class="o">/</span><span class="n">nextflow</span><span class="o">.</span><span class="n">nf</span> <span class="o">--</span><span class="nb">input</span> <span class="p">[</span><span class="n">path</span> <span class="n">to</span> <span class="n">your</span> <span class="n">data</span><span class="p">]</span>
</pre></div>
</div>
</li>
</ol>
</section>
</section>


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<li class="toctree-l2"><a class="reference internal" href="#docker-container-installation-and-usage">Docker Container Installation and Usage</a></li>
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